The adulteration of fish and seafood products, in general, is a global challenge that is constantly increasing. Seafood fraud usually involves adulteration or substitution of a type of species with the meat of lower nutritional value and quality, and therefore of the lower price, aiming for economic profit. For these reasons, sensitive, fast, simple, inexpensive and effective analytical methods is required to confirm the species origin of seafood based products. In this study, we developed species specific molecular markers such as PCR-RFLP, PCR-AFLP, and SSCP for the authentication of commercially important seer fish (Scomberomorus commerson), which is often substitute by the meat of cobia (Rachycentron canadum) and catfish (Pangasius). For this, PCR was performed using specific primers C-CB285Df and C-CB431R that amplified successfully a fragment of 147bp of the target cytochrome b gene. The amplified product was further used for developing RFLP, AFLP and SSCP markers. The developed markers give distinct band pattern and for the seer fish the unique pattern was remained same in the processed products without any degradation or alteration in the major fragments. The method was validated with 20 commercial fish products. The developed protocol can be performed within 8h to authenticate seer fish commonly adulterated seafood restaurants with cheaper catfish and cobia.